report.bib

%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/


%% Created for falks at 2015-07-22 23:03:15 +1000 


%% Saved with string encoding Unicode (UTF-8) 

@IEEEtranBSTCTL{IEEEBSTcontrol,
    CTLuse_forced_etal = "yes",
    CTLmax_names_forced_etal = "4",
    CTLnames_show_etal = "3",
}



@article{gillespie1977,
	Author = {Gillespie, Daniel T.},
	Doi = {10.1021/j100540a008},
	Eprint = {http://dx.doi.org/10.1021/j100540a008},
	Journal = {J. Phys. Chem.},
	Number = {25},
	Pages = {2340--2361},
	Title = {Exact stochastic simulation of coupled chemical reactions},
	Url = {http://dx.doi.org/10.1021/j100540a008},
	Volume = {81},
	Year = {1977},
	Bdsk-Url-1 = {http://dx.doi.org/10.1021/j100540a008}}

@article{hucka2015promoting,
	Author = {Hucka, Michael and Nickerson, David P and Bader, Gary D and Bergmann, Frank T and Cooper, Jonathan and Demir, Emek and Garny, Alan and Golebiewski, Martin and Myers, Chris J and Schreiber, Falk and others},
	Date-Modified = {2015-07-02 03:10:12 +0000},
	Journal = {Front. Bioeng. Biotechnol.},
	Publisher = {Frontiers Media SA},
	Title = {Promoting coordinated development of community-based information standards for modeling in biology: the {COMBINE} initiative},
	Volume = {3},
	Year = {2015}}

@article{courtot2011controlled,
	Author = {Courtot, M{\'e}lanie and Juty, Nick and Kn{\"u}pfer, Christian and Waltemath, Dagmar and Zhukova, Anna and Dr{\"a}ger, Andreas and Dumontier, Michel and Finney, Andrew and Golebiewski, Martin and Hastings, Janna and others},
	Journal = {Mol. Syst. Biol.},
	Number = {1},
	Pages = {543},
	Publisher = {EMBO Press},
	Title = {Controlled vocabularies and semantics in systems biology},
	Volume = {7},
	Year = {2011}}

@misc{SBMLArrays,
        title = {{SBML Level~3 Package Specification: Arrays (Draft of April 6, 2015)}},
        author = {Leandro Watanabe and Chris J. Myers and Lucian P. Smith},
        year = {2015},
        url = {http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/arrays},
        note = {Accessed: 2015-05-25}
}

@misc{SBMLMulti,
        title = {{SBML Level~3 Package Specification: Multistate/Multicomponent Species (Version 1, Release 0.1 Draft 369)}},
        author = {Fengkai Zhang and Martin Meier-Schellersheim},
        year = {2015},
        url = {http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/multi},
        note = {Accessed: 2015-05-25}
}

@webpage{COMBINE2012,
	Author = {{COMBINE}},
	Date-Added = {2015-06-15 03:34:58 +0000},
	Date-Modified = {2015-06-15 03:38:07 +0000},
	Title = {{COMBINE 2012}},
	Url = {http://co.mbine.org/events/COMBINE_2012},
	Bdsk-Url-1 = {http://co.mbine.org/events/COMBINE_2012}}

@webpage{wholeCell,
	Author = {Karr, J R and Sanghvi, J C and Macklin, D N and Jacobs, J M and Covert, M W},
	Date-Added = {2015-06-18 03:34:58 +0000},
	Date-Modified = {2015-06-18 03:38:07 +0000},
	Title = {{Whole-Cell model version 1.1}},
	Url = {https://github.com/CovertLab/WholeCell/releases/tag/v1.1},
	Bdsk-Url-1 = {https://github.com/CovertLab/WholeCell/releases/tag/v1.1}}

@article{IerselVCBBLDSDMFAMMKNS12,
	Author = {Martijn P. van Iersel and Alice Vill{\'e}ger and Tobias Czauderna and Sarah E. Boyd and Frank T. Bergmann and Augustin Luna and Emek Demir and Anatoly A. Sorokin and Ugur Dogrus{\"o}z and Yukiko Matsuoka and Akira Funahashi and Mirit I. Aladjem and Huaiyu Mi and Stuart L. Moodie and Hiroaki Kitano and Nicolas {Le Nov\`{e}re} and Falk Schreiber},
	Date-Added = {2015-06-15 03:27:31 +0000},
	Date-Modified = {2015-06-15 03:28:57 +0000},
	Journal = {Bioinformatics},
	Number = {15},
	Pages = {2016--2021},
	Title = {Software support for {SBGN} maps: {SBGN-ML} and {LibSBGN}},
	Volume = {28},
	Year = {2012}}

@article{LeNovereHMMSS09,
	Author = {Nicolas {Le Nov\`{e}re} and Michael Hucka and Huaiyu Mi and Stuart Moodie and Falk Schreiber and Anatoly Sorokin and Emek Demir and Katja Wegner and Mirit Aladjem and Sarala M. Wimalaratne and Frank T. Bergman and Ralph Gauges and Peter Ghazal and Hideya Kawaji and Lu Li and Yukiko Matsuoka and Alice Vill\'{e}ger and Sarah E. Boyd and Laurence Calzone and Melanie Courtot and Ugur Dogrusoz and Tom Freeman and Akira Funahashi and Samik Ghosh and Akiya Jouraku and Sohyoung Kim and Fedor Kolpakov and Augustin Luna and Sven Sahle and Esther Schmidt and Steven Watterson and Guanming Wu and Igor Goryanin and Douglas B. Kell and Chris Sander and Herbert Sauro and Jacky L. Snoep and Kurt Kohn and Hiroaki Kitano},
	Date-Added = {2015-06-12 03:17:02 +0000},
	Date-Modified = {2015-07-22 13:00:44 +0000},
	Journal = {Nat. Biotechnol.},
	Pages = {735--741},
	Title = {The {S}ystems {B}iology {G}raphical {N}otation},
	Volume = {27},
	Year = {2009}}

@article{Klipp07,
	Annote = {10.1038/nbt0407-390},
	Author = {Klipp, Edda and Liebermeister, Wolfram and Helbig, Anselm and Kowald, Axel and Schaber, Jorg},
	Date-Added = {2015-06-12 01:16:26 +0000},
	Date-Modified = {2015-07-02 03:10:41 +0000},
	Journal = {Nat. Biotechnol.},
	Number = {4},
	Pages = {390--391},
	Publisher = {Nature Publishing Group},
	Title = {Systems biology standards---the community speaks},
	Volume = {25},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nbt0407-390}}

@article{sedml2011,
	Author = {Waltemath, Dagmar and Adams, Richard and Bergmann, Frank and Hucka, Michael and Kolpakov, Fedor and Miller, Andrew and Moraru, Ion and Nickerson, David and Sahle, Sven and Snoep, Jacky and Le Nov\`{e}re, Nicolas},
	Date-Modified = {2015-06-15 03:11:13 +0000},
	Journal = {BMC Syst. Biol.},
	Number = {1},
	Pages = {198},
	Publisher = {BioMed Central Ltd},
	Title = {Reproducible computational biology experiments with {SED-ML}---the {S}imulation {E}xperiment {D}escription {M}arkup {L}anguage},
	Volume = {5},
	Year = {2011}}

@article{cuellar2003overview,
	Author = {Cuellar, Autumn A and Lloyd, Catherine M and Nielsen, Poul F and Bullivant, David P and Nickerson, David P and Hunter, Peter J},
	Journal = {Simulation},
	Number = {12},
	Pages = {740--747},
	Publisher = {Sage Publications},
	Title = {An overview of {CellML} 1.1, a biological model description language},
	Volume = {79},
	Year = {2003}}

@article{hucka2003,
	Author = {Hucka, Michael and Finney, Andrew and Sauro, Herbert M. and Bolouri, Hamid and Doyle, John C. and Kitano, Hiroaki and Arkin, Adam P. and Bornstein, Benjamin J. and Bray, Dennis and Cornish-Bowden, Athel and Cuellar, Autumn A. and Dronov, Sergey and Gilles, Ernst-Dieter and Ginkel, Martin and Gor, Victoria and Goryanin, Igor I. and Hedley, Warren J. and Hodgman, T. Charles and Hofmeyr, Jan-Hendrik. and Hunter, Peter J. and Juty, Nick S. and Kasberger, J. L. and Kremling, Andreas and Kummer, Ursula and Le Nov\`{e}, Nicolas  and Loew, Leslie M. and Lucio, Daniel and Mendes, Pedro and Mjolsness, Eric D. and Nakayama, Y. and Nelson, Melanie R. and Nielsen, Poul F. and Sakurada, Takeshi and Schaff, James C. and Shapiro, Bruce E. and Shimizu, Thomas S. and Spence, Hugh D. and Stelling, J\"{o}rg and Takahashi, Koichi and Tomita, Masaru and Wagner, John and Wang, J.},
	Date-Modified = {2015-07-02 03:09:48 +0000},
	Journal = {Bioinformatics},
	Number = {4},
	Pages = {524--531},
	Title = {The {Systems Biology Markup Language} ({SBML}): A Medium for Representation and Exchange of Biochemical Network Models},
	Volume = {19},
	Year = {2003}}

@article{sbo2013,
	Author = {Courtot, M{\'e}lanie and Juty, Nick and Kn{\"u}pfer, Christian and Waltemath, Dagmar and Zhukova, Anna and Dr{\"a}ger, Andreas and Dumontier, Michel and Finney, Andrew and Golebiewski, Martin and Hastings, Janna and others},
	Journal = {Mol. Syst. Biol.},
	Number = {1},
	Publisher = {Wiley Online Library},
	Title = {Controlled vocabularies and semantics in systems biology},
	Volume = {7},
	Year = {2011}}

@article{mim2001,
	Author = {Kohn, Kurt W.},
	Doi = {http://dx.doi.org/10.1063/1.1338126},
	Journal = {Chaos},
	Number = {1},
	Pages = {84--97},
	Title = {Molecular interaction maps as information organizers and simulation guides},
	Volume = {11},
	Year = {2001},
	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1338126}}

@article{path2models2013,
	Author = {B{\"u}chel, Finja and Rodriguez, Nicolas and Swainston, Neil and Wrzodek, Clemens and Czauderna, Tobias and Keller, Roland and Mittag, Florian and Schubert, Michael and Glont, Mihai and Golebiewski, Martin and van Iersel, Martijn and Keating, Sarah and Rall, Matthias and Wybrow, Michael and Hermjakob, Henning and Hucka, Michael and Kell, Douglas and M{\"u}ller, Wolfgang and Mendes, Pedro and Zell, Andreas and Chaouiya, Claudine and Saez-Rodriguez, Julio and Schreiber, Falk and Laibe, Camille and Dr{\"a}ger, Andreas and Le Nov\`{e}re, Nicolas},
	Date-Modified = {2015-07-22 13:03:15 +0000},
	Doi = {10.1186/1752-0509-7-116},
	Journal = {BMC Syst. Biol.},
	Number = {1},
	Pages = {116},
	Title = {{Path2Models}: large-scale generation of computational models from biochemical pathway maps},
	Volume = {7},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1752-0509-7-116}}

@article{chelliah2015biomodels,
	Author = {Chelliah, Vijayalakshmi and Juty, Nick and Ajmera, Ishan and Ali, Raza and Dumousseau, Marine and Glont, Mihai and Hucka, Michael and Jalowicki, Ga{\"e}l and Keating, Sarah and Knight-Schrijver, Vincent and others},
	Date-Modified = {2015-07-22 12:38:03 +0000},
	Journal = {Nucleic Acids Res.},
	Number = {D1},
	Pages = {D542--D548},
	Publisher = {Oxford Univ Press},
	Title = {{BioModels}: ten-year anniversary},
	Volume = {43},
	Year = {2015}}

@article{juty2015biomodels,
	Author = {Juty, N and Ali, R and Glont, M and Keating, S and Rodriguez, N and Swat, MJ and Wimalaratne, SM and Hermjakob, H and Le Nov{\`e}re, N and Laibe, C and others},
	Journal = {CPT Pharmacometrics Syst. Pharmacol.},
	Number = {2},
	Pages = {1--14},
	Publisher = {Wiley Online Library},
	Title = {{BioModels}: Content, Features, Functionality, and Use},
	Volume = {4},
	Year = {2015}}

@article{henkel2014combining,
	Author = {Henkel, Ron and Wolkenhauer, Olaf and Walthemath, Dagmar},
	Doi = {10.7287/peerj.preprints.376v2},
	Journal = {PeerJ PrePrints},
	Number = {e376v2},
	Title = {Combining computational models, semantic annotations, and associated simulation experiments in a graph database},
	Volume = {2},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.7287/peerj.preprints.376v2}}

@article{le2009systems,
	Author = {Le Nov\`{e}re, Nicolas and Hucka, Michael and Mi, Huaiyu and Moodie, Stuart and Schreiber, Falk and Sorokin, Anatoly and Demir, Emek and Wegner, Katja and Aladjem, Mirit I and Wimalaratne, Sarala M and others},
	Date-Modified = {2015-07-22 13:00:29 +0000},
	Journal = {Nat. Biotechnol.},
	Number = {8},
	Pages = {735--741},
	Publisher = {Nature Publishing Group},
	Title = {The {S}ystems {B}iology {G}raphical {N}otation},
	Volume = {27},
	Year = {2009}}

@article{yu:2011,
	Author = {Yu, Tommy and Lloyd, Catherine M. and Nickerson, David P. and Cooling, Michael T. and Miller, Andrew K. and Garny, Alan and Terkildsen, Jonna R. and Lawson, James and Britten, Randall D. and Hunter, Peter J. and Nielsen, Poul M F.},
	Doi = {10.1093/bioinformatics/btq723},
	Journal = {Bioinformatics},
	Month = {Mar},
	Number = {5},
	Pages = {743--744},
	Title = {The {P}hysiome {M}odel {R}epository 2},
	Volume = {27},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/btq723}}

@article{sansone2012toward,
	Author = {Sansone, Susanna-Assunta and Rocca-Serra, Philippe and Field, Dawn and Maguire, Eamonn and Taylor, Chris and Hofmann, Oliver and Fang, Hong and Neumann, Steffen and Tong, Weida and Amaral-Zettler, Linda and others},
	Journal = {Nat. Genet.},
	Number = {2},
	Pages = {121--126},
	Publisher = {Nature Publishing Group},
	Title = {Toward interoperable bioscience data},
	Volume = {44},
	Year = {2012}}

@article{lefranc_2012,
	Author = {Le Franc, Yann and Davison, Andrew P. and Gleeson, Padraig and Imam, Fahim T. and Kriener, Birgit and Larson, Stephen D. and Ray, Subhasis and Schwabe, Lars and Hill, Sean and De Schutter, Erik},
	Doi = {10.1186/1471-2202-13-S1-P149},
	Journal = {BMC Neurosci.},
	Number = {Suppl 1},
	Pages = {P149},
	Publisher = {BioMed Central Ltd},
	Title = {{Computational Neuroscience Ontology}: a new tool to provide semantic meaning to your models},
	Volume = {13},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2202-13-S1-P149}}

@article{christie_2009,
	Author = {Christie, G. Richard and Nielsen, Poul M. F. and Blackett, Shane A. and Bradley, Chris P. and Hunter, Peter J.},
	Doi = {10.1098/rsta.2009.0025},
	Journal = {Philos. Trans. R. Soc. Lond. A},
	Number = {1895},
	Pages = {1869--1884},
	Title = {{FieldML}: concepts and implementation},
	Volume = {367},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rsta.2009.0025}}

@article{britten_2013,
	Address = {United States},
	Author = {Britten, Randall D. and Christie, G. Richard and Little, Caton and Miller, Andrew K. and Bradley, Chris and Wu, Alan and Yu, Tommy and Hunter, Peter and Nielsen, Poul},
	Doi = {10.1007/s11517-013-1097-7},
	Journal = {Med. Biol. Eng. Comput.},
	Number = {11},
	Pages = {1191--1207},
	Title = {{FieldML}, a proposed open standard for the {Physiome} project for mathematical model representation},
	Volume = {51},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s11517-013-1097-7}}

@misc{gpml_2014,
	Howpublished = {\url{http://developers.pathvisio.org/wiki/EverythingGpml}},
	Title = {{GPML} Pathway Format},
	Year = {2014}}

@article{gleeson_2010,
	Author = {Gleeson, Padraig and Crook, Sharon and Cannon, Robert {C}. and Hines, Michael L. and Billings, Guy O. and Farinella, Matteo and Morse, Thomas M. and Davison, Andrew P. and Ray, Subhasis and Bhalla, Upinder S. and Barnes, Simon R. and Dimitrova, Yoana D. and Silver, R. Angus},
	Doi = {10.1371/journal.pcbi.1000815},
	Journal = {PLoS Comput. Biol.},
	Number = {6},
	Pages = {e1000815},
	Title = {{NeuroML}: a language for describing data driven models of neurons and networks with a high degree of biological detail},
	Volume = {6},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1000815}}

@article{dada_2010,
	Author = {Dada, Joseph O. and Spasic, Irena. and Paton, Norman W. and Mendes, Pedro},
	Doi = {10.1093/bioinformatics/btq069},
	Journal = {Bioinformatics},
	Number = {7},
	Pages = {932--938},
	Title = {{SBRML}: a markup language for associating systems biology data with models},
	Volume = {26},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/btq069}}

@article{hermjakob2004hupo,
	Author = {Hermjakob, Henning and Montecchi-Palazzi, Luisa and Bader, Gary and Wojcik, Jerome and Salwinski, Lukasz and Ceol, Arnaud and Moore, Susan and Orchard, Sandra and Sarkans, Ugis and von Mering, Christian and others},
	Journal = {Nat. Biotechnol.},
	Number = {2},
	Pages = {177--183},
	Publisher = {Nature Publishing Group},
	Title = {The {HUPO} {PSI}'s molecular interaction format--a community standard for the representation of protein interaction data},
	Volume = {22},
	Year = {2004}}

@article{richmond2014model,
	Author = {Richmond, Paul and Cope, Alex and Gurney, Kevin and Allerton, David J},
	Journal = {Neuroinformatics},
	Number = {2},
	Pages = {307--323},
	Publisher = {Springer},
	Title = {From model specification to simulation of biologically constrained networks of spiking neurons},
	Volume = {12},
	Year = {2014}}

@article{funahashi2008celldesigner,
	Author = {Funahashi, Akira and Matsuoka, Yukiko and Jouraku, Akiya and Morohashi, Mineo and Kikuchi, Norihiro and Kitano, Hiroaki},
	Journal = {Proc. IEEE},
	Number = {8},
	Pages = {1254--1265},
	Publisher = {IEEE},
	Title = {{CellDesigner} 3.5: a versatile modeling tool for biochemical networks},
	Volume = {96},
	Year = {2008}}

@article{waltemath2014meeting,
	Author = {Waltemath, Dagmar and Bergmann, Frank T and Chaouiya, Claudine and Czauderna, Tobias and Gleeson, Padraig and Goble, Carole and Golebiewski, Martin and Hucka, Mickael and Juty, Nick and Krebs, Olga and others},
	Journal = {Stand. Genomic Sci.},
	Number = {3},
	Title = {Meeting report from the fourth meeting of the {Computational Modeling in Biology Network} ({COMBINE})},
	Volume = {9},
	Year = {2014}}

@article{le2011meeting,
	Author = {Le Nov{\`e}re, Nicolas and Hucka, Michael and Anwar, Nadia and Bader, Gary D and Demir, Emek and Moodie, Stuart and Sorokin, Anatoly},
	Journal = {Stand. Genomic Sci.},
	Number = {2},
	Pages = {230},
	Publisher = {Genomic Standards Consortium},
	Title = {Meeting report from the first meetings of the {Computational Modeling in Biology Network} ({COMBINE})},
	Volume = {5},
	Year = {2011}}

@article{pathguide,
	Author = {Gary D. Bader and Michael P. Cary and Chris Sander},
	Journal = {Nucleic Acids Res.},
	Page = {D504--D506},
	Title = {{Pathguide: a pathway resource list}},
	Volume = {34 (Database issue)},
	Year = 2006}

@article{demir2010biopax,
	Author = {Demir, Emek and Cary, Michael P. and Paley, Suzanne and Fukuda, Ken and Lemer, Christian and Vastrik, Imre and Wu, Guanming N. and D'Eustachio, Peter and Schaefer, Carl and Luciano, Joanne and Schacherer, Frank and Martinez-Flores, Irma and Hu, Zhenzjun J. and Jimenez-Jacinto, Veronica and Joshi-Tope, Geeta and Kandasamy, Kumaran and Lopez-Fuentes, Alejandra {C}. and Mi, Huaiyu Y. and Pichler, Elgar and Rodchenkov, Igor and Splendiani, Andrea and Tkachev, Sasha and Zucker, Jeremy and Gopinath, Gopal and Rajasimha, Harsha and Ramakrishnan, Ranjani and Shah, Imran and Syed, Mustafa and Anwar, Nadia and Babur, \"{O}zg\"{u}n O. and Blinov, Michael and Brauner, Erik and Corwin, Dan and Donaldson, Sylva and Gibbons, Frank and Goldberg, Robert and Hornbeck, Peter and Luna, Augustin and Murray-Rust, Peter and Neumann, Eric and Reubenacker, Oliver and Samwald, Matthias and van Iersel, Martijn and Wimalaratne, Sarala and Allen, Keith and Braun, Burk and Whirl-Carrillo, Michelle and Cheung, Kei-Hoi H. and Dahlquist, Kam and Finney, Andrew and Gillespie, Marc and Glass, Elizabeth and Gong, Li and Haw, Robin and Honig, Michael and Hubaut, Olivier and Kane, David and Krupa, Shiva and Kutmon, Martina and Leonard, Julie and Marks, Debbie and Merberg, David and Petri, Victoria and Pico, Alex and Ravenscroft, Dean and Ren, Liya Y. and Shah, Nigam and Sunshine, Margot and Tang, Rebecca and Whaley, Ryan and Letovksy, Stan and Buetow, Kenneth H. and Rzhetsky, Andrey and Schachter, Vincent and Sobral, Bruno S. and Dogrusoz, Ugur and McWeeney, Shannon and Aladjem, Mirit and Birney, Ewan and Collado-Vides, Julio and Goto, Susumu and Hucka, Michael and Le Nov\`{e}re, Nicolas and Maltsev, Natalia and Pandey, Akhilesh and Thomas, Paul and Wingender, Edgar and Karp, Peter D. and Sander, Chris and Bader, Gary D.},
	Doi = {10.1038/nbt.1666},
	Journal = {Nat. Biotechnol.},
	Number = {9},
	Pages = {935--942},
	Title = {The {B}io{P}{A}{X} community standard for pathway data sharing},
	Volume = {28},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nbt.1666}}

@article{galdzicki2014,
	Author = {Galdzicki, Michal and Clancy, Kevin P. and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline Y. and Rodriguez, Cesar A. and Roehner, Nicholas and Wilson, Mandy L. and Adam, Laura and Anderson, J. Christopher and Bartley, Bryan A. and Beal, Jacob and Chandran, Deepak and Chen, Joanna and Densmore, Douglas and Endy, Drew and Gr\"{u}nberg, Raik and Hallinan, Jennifer and Hillson, Nathan J. and Johnson, Jeffrey D. and Kuchinsky, Allan and Lux, Matthew and Misirli, Goksel and Peccoud, Jean and Plahar, Hector A. and Sirin, Evren and Stan, Guy-Bart, B. and Villalobos, Alan and Wipat, Anil and Gennari, John H. and Myers, Chris J. and Sauro, Herbert M.},
	Doi = {10.1038/nbt.2891},
	Journal = {Nat. Biotechnol.},
	Number = {6},
	Pages = {545},
	Publisher = {Nature Publishing Group},
	Title = {The {Synthetic Biology Open Language} ({SBOL}) provides a community standard for communicating designs in synthetic biology},
	Volume = {32},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nbt.2891}}

@misc{mamo_2014,
	Author = {Anna Zhukova and Dagmar Waltemath and Maciej J. Swat and Jon Olav Vik and Nicolas Rodriguez and Nicolas {Le Nov\`{e}re}},
	Howpublished = {\url{https://sourceforge.net/p/mamo-ontology/wiki/Home/}},
	Title = {{Mathematical Modelling Ontology} ({MAMO})},
	Year = {2014}}

@article{Eilbeck2005,
	Author = {Eilbeck, Karen and Lewis, Suzanna E. and Mungall, Christopher J. and Yandell, Mark and Stein, Lincoln and Durbin, Richard and Ashburner, Michael},
	Doi = {10.1186/gb-2005-6-5-r44},
	Journal = {Genome Biol.},
	Number = {5},
	Pages = {R44},
	Title = {The {Sequence Ontology}: a tool for the unification of genome annotations},
	Volume = {6},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/gb-2005-6-5-r44}}

@article{Juty2012,
	Author = {Nick Juty and Nicolas Le Nov\`{e}re and Camille Laibe},
	Doi = {10.1093/nar/gkr1097},
	Journal = {Nucleic Acids Res.},
	Month = {Jan},
	Number = {Database issue},
	Pages = {D580--D586},
	Title = {Identifiers.org and {MIRIAM Registry}: community resources to provide persistent identification},
	Volume = {40},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/nar/gkr1097}}

@article{courtot2011a,
	Author = {Courtot, M\'{e}lanie and Juty, Nick and Kn\"upfer, Christian and Waltemath, Dagmar and Zhukova, Anna and Dr\"ager, Andreas and Dumontier, Michel and Finney, Andrew and Golebiewski, Martin and Hastings, Janna and Hoops, Stefan and Keating, Sarah and Kell, Douglas B. and Kerrien, Samuel and Lawson, James and Lister, Allyson and Lu, James and Machne, Rainer and Mendes, Pedro and Pocock, Matthew and Rodriguez, Nicolas and Vill\'{e}ger, Alice and Wilkinson, Darren J. and Wimalaratne, Sarala and Laibe, Camille and Hucka, Michael and Le Nov\`{e}re, Nicolas},
	Date-Modified = {2015-07-02 03:13:51 +0000},
	Doi = {10.1038/msb.2011.77},
	Journal = {Mol. Syst. Biol.},
	Number = 1,
	Pages = 543,
	Title = {Controlled vocabularies and semantics in systems biology},
	Volume = 7,
	Year = 2011,
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/msb.2011.77}}

@article{vaniersel_2008,
	Author = {van Iersel, Martijn P. and Kelder, Thomas and Pico, Alexander R. and Hanspers, Kristina and Coort, Susan and Conklin, Bruce R. and Evelo, Chris},
	Doi = {10.1186/1471-2105-9-399},
	Journal = {BMC Bioinformatics},
	Pages = {399},
	Title = {Presenting and exploring biological pathways with {PathVisio}},
	Volume = {9},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2105-9-399}}

@misc{mathml,
	Author = {Ausbrooks, Ron and Buswell, Stephen and Dalmas, St\~{A}\copyrightphane and Devitt, Stan and Diaz, Angel and Hunter, Roger and Smith, Bruce and Soiffer, Neil and Sutor, Robert and Watt, Stephen},
	Howpublished = {\url{http://www.w3.org/TR/2003/REC-MathML2-20031021/}},
	Title = {{M}athematical {M}arkup {L}anguage ({M}ath{M}{L}) Version 2.0 (Second Edition) {{W3C}} Recommendation 21 {O}ctober 2003},
	Year = {2003}}

@misc{lassila_1999,
	Author = {Lassila, Ora and Swick, Ralph},
	Howpublished = {\url{http://www.w3.org/TR/REC-rdf-syntax/}},
	Title = {Resource Description Framework ({RDF}) Model and Syntax Specification},
	Url = {http://www.w3.org/TR/REC-rdf-syntax/},
	Year = {1999},
	Bdsk-Url-1 = {http://www.w3.org/TR/REC-rdf-syntax/}}

@article{go_2000,
	Author = {{The Gene Ontology Consortium}},
	Journal = {Nat. Genet.},
	Pages = {25--29},
	Title = {{Gene Ontology}: tool for the unification of biology},
	Volume = {25},
	Year = {2000}}

@article{hermjakob_2004,
	Author = {Hermjakob, H. and Montecchi-Palazzi, L. and Bader, G. and Wojcik, R. and Salwinski, L. and Ceol, A. and Moore, S. and Orchard, S. and Sarkans, U. and von Mering, {C}. and Roechert, B. and Poux, S. and Jung, E. and Mersch, H. and Kersey, P. and Lappe, M. and Li, YX X. and Zeng, R. and Rana, D. and Nikolski, M. and Husi, H. and Brun, {C}. and Shanker, K. and Grant, SGN G. N. and Sander, {C}. and Bork, P. and Zhu, WM M. and Pandey, A. and Brazma, A. and Jacq, B. and Vidal, M. and Sherman, D. and Legrain, P. and Cesareni, G. and Xenarios, L. and Eisenberg, D. and Steipe, B. and Hogue, {C}. and Apweiler, R.},
	Doi = {10.1038/nbt926},
	Journal = {Nat. Biotechnol.},
	Number = {2},
	Pages = {177--183},
	Title = {The {HUPO} {PSI}'s {Molecular Interaction} format---a community standard for the representation of protein interaction data},
	Volume = {22},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nbt926}}

@article{montecchipalazzi_2008,
	Author = {Montecchi-Palazzi, Luisa and Beavis, Ron and Binz, Pierre-Alain and Chalkley, Robert J. and Cottrell, John and Creasy, David and Shofstahl, Jim and Seymour, Sean L. and Garavelli, John S.},
	Doi = {10.1038/nbt0808-864},
	Journal = {Nat. Biotechnol.},
	Number = {8},
	Pages = {864--866},
	Title = {The {PSI}-{MOD} community standard for representation of protein modification data},
	Volume = {26},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nbt0808-864}}

@misc{Bergmann2014combine,
	Author = {Bergmann, Frank T. and Adams, Richard and Moodie, Stuart and Cooper, Jonathan and Glont, Mihai and Golebiewski, Martin and Hucka, Michael and Laibe, Camille and Miller, Andrew K. and Nickerson, David P. and Olivier, Brett G. and Rodriguez, Nicolas and Sauro, Herbert M. and Scharm, Martin and Soiland-Reyes, Stian and Waltemath, Dagmar and Yvon, Florent and Nov\`{e}re, Nicolas Le},
	Howpublished = {arXiv:1407.4992 [cs.DL]},
	Title = {One file to share them all: Using the {COMBINE} Archive and the {OMEX} format to share all information about a modeling project},
	Year = {2014}}

@article{hucka_2003,
	Author = {Hucka, Michael and Finney, Andrew and Sauro, Herbert M. and Bolouri, Hamid and Doyle, John C. and Kitano, Hiroaki and Arkin, Adam P. and Bornstein, Benjamin J. and Bray, Dennis and Cornish-Bowden, Athel and Cuellar, Autumn A. and Dronov, Sergey and Gilles, Ernst-Dieter and Ginkel, Martin and Gor, Victoria and Goryanin, Igor I. and Hedley, Warren J. and Hodgman, T. Charles and Hofmeyr, Jan-Hendrik. and Hunter, Peter J. and Juty, Nick S. and Kasberger, J. L. and Kremling, Andreas and Kummer, Ursula and Nov\`{e}re, Nicolas Le and Loew, Leslie M. and Lucio, Daniel and Mendes, Pedro and Mjolsness, Eric D. and Nakayama, Y. and Nelson, Melanie R. and Nielsen, Poul F. and Sakurada, Takeshi and Schaff, James C. and Shapiro, Bruce E. and Shimizu, Thomas S. and Spence, Hugh D. and Stelling, J\"{o}rg and Takahashi, Koichi and Tomita, Masaru and Wagner, John and Wang, J.},
	Date-Modified = {2015-07-02 03:08:57 +0000},
	Journal = {Bioinformatics},
	Number = {4},
	Pages = {524--531},
	Title = {The {Systems Biology Markup Language} ({SBML}): A Medium for Representation and Exchange of Biochemical Network Models},
	Volume = {19},
	Year = {2003}}

@article{hucka_2004,
	Author = {Hucka, Michael and Finney, Andrew and Bornstein, Benjamin J. and Keating, Sarah M. and Shapiro, Bruce E. and Matthews, Joanne and Kovitz, Ben L. and Schilstra, Maria J. and Funahashi, Akira and Doyle, John C. and Kitano, Hiroaki},
	Date = {June},
	Date-Modified = {2015-07-02 03:09:09 +0000},
	Journal = {BMC Syst. Biol.},
	Number = {1},
	Pages = {41--53},
	Title = {Evolving a Lingua Franca and Associated Software Infrastructure for Computational Systems Biology: The {Systems} {Biology} {Markup} {Language} ({SBML}) Project},
	Volume = {1},
	Year = {2004}}

@misc{hucka_2010,
	Author = {Hucka, Michael and Bergmann, Frank T. and Hoops, Stephan and Keating, Sarah M. and Sahle, Sven and Schaff, James {C}. and Smith, Lucian P.},
	Doi = {http://dx.doi.org/10.1038/npre.2010.4959.1},
	Howpublished = {Available via the World Wide Web at \url{http://sbml.org/Documents/Specifications}},
	Institution = {California Institute of Technology},
	Publisher = {Nature Precedings},
	Title = {The {S}ystems {B}iology {M}arkup {L}anguage ({{SBML}}): Language Specification for {L}evel 3 {V}ersion 1 {Core}},
	Uuid = {B0D5B556-96A3-4589-B634-30652305AC5F},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/npre.2010.4959.1}}

@article{demir2010,
	Author = {Demir, Emek and Cary, Michael P. and Paley, Suzanne and Fukuda, Ken and Lemer, Christian and Vastrik, Imre and Wu, Guanming N. and D'Eustachio, Peter and Schaefer, Carl and Luciano, Joanne and Schacherer, Frank and Martinez-Flores, Irma and Hu, Zhenzjun J. and Jimenez-Jacinto, Veronica and Joshi-Tope, Geeta and Kandasamy, Kumaran and Lopez-Fuentes, Alejandra {C}. and Mi, Huaiyu Y. and Pichler, Elgar and Rodchenkov, Igor and Splendiani, Andrea and Tkachev, Sasha and Zucker, Jeremy and Gopinath, Gopal and Rajasimha, Harsha and Ramakrishnan, Ranjani and Shah, Imran and Syed, Mustafa and Anwar, Nadia and Babur, \"{O}zg\"{u}n O. and Blinov, Michael and Brauner, Erik and Corwin, Dan and Donaldson, Sylva and Gibbons, Frank and Goldberg, Robert and Hornbeck, Peter and Luna, Augustin and Murray-Rust, Peter and Neumann, Eric and Reubenacker, Oliver and Samwald, Matthias and van Iersel, Martijn and Wimalaratne, Sarala and Allen, Keith and Braun, Burk and Whirl-Carrillo, Michelle and Cheung, Kei-Hoi H. and Dahlquist, Kam and Finney, Andrew and Gillespie, Marc and Glass, Elizabeth and Gong, Li and Haw, Robin and Honig, Michael and Hubaut, Olivier and Kane, David and Krupa, Shiva and Kutmon, Martina and Leonard, Julie and Marks, Debbie and Merberg, David and Petri, Victoria and Pico, Alex and Ravenscroft, Dean and Ren, Liya Y. and Shah, Nigam and Sunshine, Margot and Tang, Rebecca and Whaley, Ryan and Letovksy, Stan and Buetow, Kenneth H. and Rzhetsky, Andrey and Schachter, Vincent and Sobral, Bruno S. and Dogrusoz, Ugur and McWeeney, Shannon and Aladjem, Mirit and Birney, Ewan and Collado-Vides, Julio and Goto, Susumu and Hucka, Michael and Le Nov\`{e}re, Nicolas and Maltsev, Natalia and Pandey, Akhilesh and Thomas, Paul and Wingender, Edgar and Karp, Peter D. and Sander, Chris and Bader, Gary D.},
	Doi = {10.1038/nbt.1666},
	Journal = {Nat. Biotechnol.},
	Number = {9},
	Pages = {935--942},
	Title = {The {B}io{P}{A}{X} community standard for pathway data sharing},
	Volume = {28},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nbt.1666}}

@article{hedley_2001b,
	Author = {Hedley, Warren J. and Nelson, Melanie R. and Bullivant, D. P. and Nielson, Poul F.},
	Journal = {Philos. Trans. R. Soc. Lond. A},
	Pages = {1073--1089},
	Title = {A Short Introduction to {CellML}},
	Volume = {359},
	Year = {2001}}

@article{lenovere2006,
	Author = {Nicolas Le Nov\`{e}re},
	Journal = {BMC Neurosci.},
	Number = {Suppl. 1},
	Pages = {S11},
	Title = {Model storage, exchange and integration},
	Volume = {7},
	Year = {2006}}

@misc{sbml_process,
	Howpublished = {\url{http://sbml.org/Documents/SBML_Development_Process}},
	Title = {{SBML} Development Process},
	Year = {2014}}

@article{quackenbush_2006b,
	Author = {Quackenbush, John and Stoeckert, Christian and Ball, Catherine and Brazma, Alvis and Gentleman, Robert and Huber, Wolfgang and Irizarry, Rafael and Salit, Marc and Sherlock, Gavin and Spellman, Paul},
	Journal = {Nature},
	Number = {7080},
	Pages = {24},
	Publisher = {Nature Publishing Group},
	Title = {Top-down standards will not serve systems biology},
	Volume = {440},
	Year = {2006}}

@article{Draeger2014a,
	Author = {Dr\"ager, Andreas and Palsson, Bernhard {\O}.},
	Doi = {10.3389/fbioe.2014.00061},
	Journal = {Front. Bioeng. Biotechnol.},
	Month = nov,
	Number = {61},
	Title = {Improving collaboration by standardization efforts in systems biology},
	Volume = {2},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fbioe.2014.00061}}

@article{farrell1986installed,
	Author = {Farrell, Joseph and Saloner, Garth},
	Journal = {Am. Econ. Rev.},
	Pages = {940--955},
	Title = {Installed base and compatibility: Innovation, product preannouncements, and predation},
	Year = {1986}}

@article{katz1985network,
	Author = {Katz, Michael L. and Shapiro, Carl},
	Journal = {Am. Econ. Rev.},
	Number = {3},
	Pages = {424--440},
	Title = {Network externalities, competition, and compatibility},
	Volume = {75},
	Year = {1985}}

@misc{nih2014,
	Author = {{National Institutes of Health}},
	Howpublished = {\url{http://grants.nih.gov/grants/guide/notice-files/NOT-CA-14-054.html}},
	Key = {NotCa14054RequestForInformation:},
	Title = {Request for Information ({RFI}): Input on Information Resources for Data-Related Standards Widely Used in Biomedical Science},
	Year = {2014}}

@article{Mendes2009,
	Author = {Mendes, P and Hoops, S and Sahle, S and Gauges, R and Dada, J and Kummer, U},
	Date-Modified = {2015-07-02 03:15:56 +0000},
	Journal = {Methods Mol. Biol.},
	Pages = {17--59},
	Title = {{Computational modeling of biochemical networks using COPASI}},
	Volume = 500,
	Year = 2009}

@article{Stevens2013,
	Author = {Stevens, J T and Myers, C J},
	Date-Modified = {2015-07-02 03:16:36 +0000},
	Journal = {ACS Synth. Biol.},
	Number = 5,
	Pages = {223--229},
	Title = {{Dynamic modeling of cellular populations within {iBioSim}}},
	Volume = 2,
	Year = 2013}

@article{Rohn2012,
	Author = {Rohn, H and Junker, A and Hartmann, A and Grafahrend-Belau, E and Treutler, H and Klapperst\"uck, M and Czauderna, T and Klukas, C and Schreiber, F},
	Date-Modified = {2015-07-02 03:24:08 +0000},
	Journal = {BMC Syst. Biol.},
	Pages = {139},
	Title = {{VANTED v2: a framework for systems biology applications}},
	Volume = {6},
	Year = {2012}}

@article{Kolpakov2006,
	Author = {Fedor Kolpakov},
	Date-Modified = {2015-07-02 03:16:08 +0000},
	Journal = {Proc. BGRS},
	Pages = {281--285},
	Title = {{BioUML}: visual modeling, automated code generation and simulation of biological systems},
	Volume = {3},
	Year = {2006}}

@article{Wolkenhauer2009,
	Author = {Wolkenhauer, O and Fell, D and De Meyts, P and Bl\"uthgen, N and Herzel, H and Le Nov\`ere, N and H\"ofer, T and Sch\"urrle, K and van Leeuwen, I},
	Date-Modified = {2015-07-02 03:17:15 +0000},
	Journal = {IET Syst. Biol.},
	Number = 3,
	Pages = {131--136},
	Title = {{SysBioMed} report: advancing systems biology for medical applications},
	Volume = 3,
	Year = 2009}

@webpage{ERASysBio2015,
	Author = {{ERASysBio consortium}},
	Date-Modified = {2015-06-15 03:38:08 +0000},
	Title = {{ERA-NET} for systems biology},
	Url = {http://www.erasysbio.net},
	Bdsk-Url-1 = {http://www.erasysbio.net}}

@webpage{CaSYM2015,
	Author = {{CaSYM consortium}},
	Date-Modified = {2015-06-15 03:37:46 +0000},
	Title = {Coordinating Action Systems Medicine: Implementation of Systems Medicine Across Europe},
	Url = {https://www.casym.eu},
	Bdsk-Url-1 = {https://www.casym.eu}}

@article{Karr2012,
	Author = {Karr, J R and Sanghvi, J C and Macklin, D N and Gutschow, M V and Jacobs, J M and Bolival, Jr, B and Assad-Garcia, N and Glass, J I and Covert, M W},
	Journal = {Cell},
	Number = {2},
	Pages = {389--401},
	Title = {A whole-cell computational model predicts phenotype from genotype},
	Volume = {150},
	Year = {2012}}

@article{Lee2009,
	Author = {Lee, D S and Burd, H and Liu, J and Almaas, E and Wiest, O and Barab\'asi, A L and Oltvai, Z N and Kapatral, V},
	Date-Modified = {2015-07-02 03:07:27 +0000},
	Journal = {J. Bacteriol.},
	Number = 12,
	Pages = {4015--4024},
	Title = {Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple \textit{Staphylococcus aureus} genomes identify novel antimicrobial drug targets},
	Volume = 191,
	Year = 2009}

@article{Lee2012,
	Author = {Lee, J W and Na, D and Park, J M and Lee, J and Choi, S and Lee, S Y},
	Date-Modified = {2015-07-02 03:07:15 +0000},
	Journal = {Nat. Chem. Biol.},
	Number = 6,
	Pages = {536--546},
	Title = {Systems metabolic engineering of microorganisms for natural and non-natural chemicals},
	Volume = 8,
	Year = 2012}

@article{Reed2006,
	Author = {Reed, J L and Patel, T R and Chen, K H and Joyce, A R and Applebee, M K and Herring, C D and Bui, O T and Knight, E M and Fong, S S and Palsson, B O},
	Date-Modified = {2015-07-02 03:06:43 +0000},
	Journal = {Proc. Natl. Acad. Sci. U. S. A.},
	Number = 46,
	Pages = {17480--17484},
	Title = {Systems approach to refining genome annotation},
	Volume = 103,
	Year = 2006}

@article{Macklin2014,
	Author = {Macklin, D N and Ruggero, N A and Covert, M W},
	Date-Modified = {2015-07-02 03:08:06 +0000},
	Journal = {Curr. Opin. Biotechnol.},
	Pages = {111--115},
	Title = {The future of whole-cell modeling},
	Volume = 28,
	Year = 2014}

@article{Karr2015,
	Author = {Karr, J R and Takahashi, K and Funahashi, A},
	Date-Modified = {2015-07-02 03:08:38 +0000},
	Journal = {Curr. Opin. Microbiol.},
	Title = {The principles of whole-cell modeling},
	Volume = {{(in press)}},
	Year = 2015}

@article{Madsen2012,
	Author = {Madsen, C and Myers, C J and Patterson, T and Roehner, N and Stevens, J T and Winstead, C},
	Date-Modified = {2015-07-22 12:40:17 +0000},
	Journal = {IEEE Des. Test Comput.},
	Number = 3,
	Title = {Design and test of genetic circuits using iBioSim},
	Volume = 29,
	Year = 2012}

@article{Hlavacek2006,
	Author = {Hlavacek, W S and Faeder, J R and Blinov, M L and Posner, R G and Hucka, M and Fontana, W},
	Date-Modified = {2015-07-22 12:40:57 +0000},
	Journal = {Sci. STKE},
	Number = 344,
	Pages = {re6},
	Title = {Rules for modeling signal-transduction systems},
	Volume = {2006},
	Year = 2006}

@article{Hogg2014,
	Author = {Hogg, J S and Harris, L A and Stover, L J and Nair, N S and Faeder, J R},
	Date-Modified = {2015-07-22 12:41:17 +0000},
	Journal = {PLoS Comput. Biol.},
	Number = 4,
	Pages = {e1003544},
	Title = {Exact hybrid particle/population simulation of rule-based models of biochemical systems},
	Volume = 10,
	Year = 2014}

@article{Sneddon2011,
	Author = {Sneddon, M W and Faeder, J R and Emonet, T},
	Date-Modified = {2015-07-22 12:41:34 +0000},
	Journal = {Nat. Methods},
	Number = 2,
	Pages = {177--183},
	Title = {Efficient modeling, simulation and coarse-graining of biological complexity with {NFsim}},
	Volume = 8,
	Year = 2011}

@article{Somogyi17062015,
	Abstract = {Motivation: This article presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML). SBML is the most widely used standard for representing dynamic networks, especially biochemical networks. libRoadRunner is fast enough to support large-scale problems such as tissue models, studies that require large numbers of repeated runs and interactive simulations.Results: libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python interface. Its Python Application Programming Interface (API) is similar to the APIs of MATLAB (www.mathworks.com) and SciPy (http://www.scipy.org/), making it fast and easy to learn. libRoadRunner uses a custom Just-In-Time (JIT) compiler built on the widely used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) including several SBML extensions (composition and distributions). It offers multiple deterministic and stochastic integrators, as well as tools for steady-state analysis, stability analysis and structural analysis of the stoichiometric matrix.Availability and implementation: libRoadRunner binary distributions are available for Mac OS X, Linux and Windows. The library is licensed under Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi. http://www.libroadrunner.org provides online documentation, full build instructions, binaries and a git source repository.Contacts: hsauro@u.washington.edu or somogyie@indiana.eduSupplementary information: Supplementary data are available at Bioinformatics online.},
	Author = {Somogyi, Endre T. and Bouteiller, Jean-Marie and Glazier, James A. and K{\"o}nig, Matthias and Medley, J. Kyle and Swat, Maciej H. and Sauro, Herbert M.},
	Doi = {10.1093/bioinformatics/btv363},
	Eprint = {http://bioinformatics.oxfordjournals.org/content/early/2015/07/13/bioinformatics.btv363.full.pdf+html},
	Journal = {Bioinformatics},
	Title = {{libRoadRunner}: a high performance {SBML} simulation and analysis library},
	Url = {http://bioinformatics.oxfordjournals.org/content/early/2015/07/13/bioinformatics.btv363.abstract},
	Year = {2015},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/early/2015/07/13/bioinformatics.btv363.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btv363}}

@article{ebrahim2013cobrapy,
	Author = {Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
	Date-Modified = {2015-07-22 12:34:47 +0000},
	Journal = {BMC Syst. Biol.},
	Number = {1},
	Pages = {74},
	Publisher = {BioMed Central Ltd},
	Title = {{COBRApy}: constraints-based reconstruction and analysis for python},
	Volume = {7},
	Year = {2013}}

@misc{sbwfba,
	Author = {Bergmann, Frank T.},
	Howpublished = {Available via the World Wide Web at \url{https://github.com/fbergmann/FluxBalance}},
	Title = {{SBW} Flux Balance},
	Year = 2012}

@misc{sedml_web_tools,
	Author = {Bergmann, Frank T.},
	Howpublished = {Available via the World Wide Web at \url{http://sysbioapps.dyndns.org/SED-ML_Web_Tools}},
	Title = {{SED-ML} Web Tools},
	Year = 2015}

@article{bornstein_2008,
	Author = {Benjamin J. Bornstein and Sarah M. Keating and Akiya Jouraku and Michael Hucka},
	Journal = {Bioinformatics},
	Number = {6},
	Pages = {880--881},
	Title = {{LibSBML: an API library for SBML}},
	Volume = {24},
	Year = 2008}

@article{Hastings2013,
	Author = {Hastings, J and de Matos, P and Dekker, A and Ennis, M and Harsha, B and Kale, N and Muthukrishnan, V and Owen, G and Turner, S and Williams, M and Steinbeck, C},
	Date-Modified = {2015-07-22 12:40:41 +0000},
	Journal = {Nucleic Acids Res.},
	Number = {Database issue},
	Pages = {D456--D463},
	Title = {The {ChEBI} reference database and ontology for biologically relevant chemistry: enhancements for 2013},
	Volume = 41,
	Year = 2013}

@article{Karr2015b,
	Author = {Karr, J R and Williams, A H and Zucker, J D and Raue, A and Steiert, B and Timmer, J and Kreutz, C and {DREAM8 Parameter Estimation Challenge Consortium} and Wilkinson, S and Allgood, B A and Bot, B M and Hoff, B R and Kellen, M R and Covert, M W and Stolovitzky, G A and Meyer, P},
	Date-Modified = {2015-07-22 12:35:49 +0000},
	Journal = {PLoS Comput. Biol.},
	Number = 5,
	Pages = {e1004096},
	Title = {Summary of the {DREAM8 Parameter Estimation Challenge}: Toward Parameter Identification for Whole-Cell Models},
	Volume = 11,
	Year = {2015}}

@article{Karr2014,
	Author = {Karr, J R and Phillips, N C and Covert, M W},
	Journal = {Database},
	Number = {pii},
	Pages = {bau095},
	Title = {{WholeCellSimDB}: a hybrid relational/HDF database for whole-cell model predictions},
	Volume = 2014,
	Year = {2014}}

@article{Sanghvi2013,
	Author = {Sanghvi, J C and Regot, S and Carrasco, S and Karr, J R and Gutschow, M V and Bolival, Jr, B and Covert, M W},
	Journal = {Nat. Methods},
	Number = {12},
	Pages = {1192--1195},
	Title = {Accelerated discovery via a whole-cell model},
	Volume = 10,
	Year = {2013}}

@article{Lee2013,
	Author = {Lee, R and Karr, J R and Covert, M W},
	Journal = {BMC Bioinformatics},
	Pages = {253},
	Title = {{WholeCellViz}: data visualization for whole-cell models},
	Volume = 14,
	Year = {2013}}

@article{Purcell2013,
	Author = {Purcell, O and Jain, B and Karr, J R and Covert, M W and Lu, T K},
	Journal = {Chaos},
	Number = {2},
	Pages = {025112},
	Title = {Towards a whole-cell modeling approach for synthetic biology},
	Volume = 23,
	Year = {2013}}

@article{Karr2013,
	Author = {Karr, J R and Sanghvi, J C and Macklin, D N and Arora, A and Covert, M W},
	Date-Modified = {2015-07-22 12:35:24 +0000},
	Journal = {Nucleic Acids Res.},
	Number = {Database issue},
	Pages = {D787--D792},
	Title = {{WholeCellKB}: model organism databases for comprehensive whole-cell models},
	Volume = 41,
	Year = {2013}}

@article{Wittig2012,
	Author = {Wittig, U and Kania, R and Golebiewski, M and Rey, M and Shi, L and Jong, L and Algaa, E and Weidemann, A and Sauer-Danzwith, H and Mir, S and Krebs, O and Bittkowski, M and Wetsch, E and Rojas, I and M{\"u}ller, W},
	Date-Modified = {2015-07-22 12:42:28 +0000},
	Journal = {Nucleic Acids Res.},
	Number = {Database issue},
	Pages = {D790--D796},
	Title = {{SABIO-RK}--database for biochemical reaction kinetics},
	Volume = 40,
	Year = 2012}

@article{Karp2010,
	Author = {Karp, P D and Paley, S M and Krummenacker, M and Latendresse, M and Dale, J M and Lee, T J and Kaipa, P and Gilham, F and Spaulding, A and Popescu, L and Altman, T and Paulsen, I and Keseler, I M and Caspi, R},
	Date-Modified = {2015-07-22 12:43:39 +0000},
	Journal = {Brief. Bioinform.},
	Number = 1,
	Pages = {40--79},
	Title = {{Pathway Tools} version 13.0: integrated software for pathway/genome informatics and systems biology},
	Volume = 11,
	Year = 2010}

@article{UniProt2015,
	Author = {{UniProt Consortium}},
	Date-Modified = {2015-07-22 12:42:43 +0000},
	Journal = {Nucleic Acids Res.},
	Number = {Database issue},
	Pages = {D204--D212},
	Title = {{UniProt}: a hub for protein information},
	Volume = 43,
	Year = 2015}

@article{Smith2009,
    journal = {Bioinformatics},
    year = 2009,
    volume = 25,
    number = 18,
    pages = {2452--2454},
    title = {{Antimony}: a modular model definition language},
    author = {Smith, L P and Bergmann, F T and Chandran, D and Sauro, H M}
    }
	
@article{Kazakiewicz2015,
	journal = {Comput. Biol. Chem.},
	year = 2015,
	volume = 58,
	number = {XX--YY},
	title = {A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium},
	author = {Kazakiewicz, D and Karr, J R and Langner, K and Plewczynski, D}
	}